Insert HTML after the body tag in JIRA

We are trying to put JIRA into Websphere Portal navigation and it works OK except the WP code must be placed right after the body tag on each page. We placed it following the article about placing Google Analytics code but it is inserted inside a header with some styling applied, this makes all text with a href links blue. To what file we should move the code to be rendered before the header and still on each page?

David, your solution works, however JIRA pages obviously load without the portal navigation and after that when script is executed, the navigation bar appears. Since it is pretty large, visual experience is far from ideal.

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